Research Project 2

Develop an improved adaptative sampling method for Nanopore dRNA and cDNA sequencing

About the Project

University of Nottingham

Nottingham, UK

Oxford Nanopore Technologies

Oxford, UK

Matt Loose

Aino Järvelin


University of Nottingham

PhD enrolment

Yearly salary

20.162,01 €

Research Objectives

Little is known about transcriptome-wide epi-transcriptomic  modifications and isoform diversity, especially of low abundance and biomedically relevant transcripts. Adaptive sampling (AS) is a strategy to enrich for specific transcripts in silico but its use in native RNA (dRNA) applications remains to be explored. Our objectives are:

  • To test and further develop experimental and informatic tools for adaptive sampling on RNA.
  • To demonstrate the utility of dRNA sequencing, enhanced by adaptive sampling, on analysis of RNA  isoforms, tail lengths, and modifications.
  • To apply these approaches to characterise transcriptome changes in a cancer cell line.

Envisioned Secondments

  • Wobble (Kuo): Methods for cDNA normalisation and rare transcript annotation.
  • CRG (Novoa): Epitranscriptomics data generation analysis.
  • CSIC (Conesa): Learn statistics.

About the Supervisors and Host Groups

Aino Järvelin


I am interested in using genomics and data science to solve biological puzzles and to advance human and environmental health. I love to design new projects, distill complex datasets into actionable and insightful patterns, and translate between people from different disciplines and backgrounds whenever I can to create something new together. I actively promote help build open and inclusive work environments that enable people to learn, grow, and communicate. You’re sure to grab my attention with a nice data viz.

My core toolkit consists of R, python, and genomics tools and databases. With a background in experimental biology, have a strong understanding of how bio(medical) data is generated and the needs of wetlab experimentalists.

Matt Loose

University of Nottingham